I've never thought of Jenova as being 'pushed around', but... she was sealed inside solid rock for two thousand years, then sealed inside a tank and used for experiments. Samples of her cells were extracted. Finally, her own 'son' cut off her head. Being dismembered like that is going to leave anyone feeling a little out of sorts.
I think Jenova was still in control of herself; Sephiroth was doing all kinds of nasty things in order to help her, but perhaps not because he was completely under her control. She needed his help - he was still relatively intact, so he could summon Meteor, control the 'Clones' and bring them to the Reunion, etc.